ShotgunFunctionalizeR is an R-package for functional comparison
of metagenomes. The package contains tools for importing,
annotating and visualising metagenomic data produced by shotgun
high-throughput sequencing. ShotgunFunctionalizeR contains
several statistical procedures for assessing functional differences between
samples, both for individual genes and for entire pathways.
In addition to standard and previously published methods, we have
developed and implemented a novel approach based on a Poisson
model. This procedure is highly flexible and thus applicable to a wide
range of different experimental designs. Further information about is
available in Kristiansson,
Hugenholtz and Dalevi 2009 or in a recent poster presented at FEMS
2009 in Gothenburg.
||ShotgunFunctionalizeR 1.2-9 is now available where a number of bugs
introduced in the latest release have been removed. Minor changes has also
been made to the reference manual.
||ShotgunFunctionalizeR 1.2-8 is now availalbe. New features include
The new version is available for Unix/Linux, Windows and Mac OS X.
- Support for PFAM, TIGRFAM and custom annotation
- Several new functions for manipulation of data objects
- Basic methodology for assessing functional diversity (rarefaction curve analysis, Chao-estimator, clustering)
- Many bugfixes, some speedups (and probably some new novel bugs as well!)
- Updated user's guide and reference manual
||ShotgunFunctionalizeR 1.0-3 is now available. This release fixes a
critical bug where annotations of gene families could, in rare situations, be mixed up. We
have also made significant changes for the p-value calculations in the
Poisson model, which will now be more robust (we now use chi-squared tests of the
residual deviance instead of Wald tests of the regression
||ShotgunFunctionalizeR 1.0-2 is now available. This release contains
mainly bug fixed.
A paper describing ShotgunFunctionalizeR has now been published in
||We have now added support for Mac OS X.
||ShotgunFunctionalizeR 1.0-1 has now been released. This version contains
a few bug fixes as well as the missing manual pages. The reference manual
has also be updated.
||ShotgunFunctionalizeR 1.0 has now been released. This version is the
first final version (which doesn't mean that it is bug free). Changes includes mostly bug fixes. The User's Guide
and Reference Manual has also been updated.
||Two example datasets (Ocean's Interior and Mouse Gut) is now available
as download in ShotgunFunctionalizeR compatible format.
||ShotgunFunctionalizeR 0.0-13 is now available.
||ShotgunFunctionalizeR 0.0-12 is available for download. New functions
include the groupPlot function (to plot results after direct comparions
between groups using the Poisson model). The User Guide has been updated
- ShotgunFunctionalizeR R-package 1.2-9 for Unix/Linux Download
- ShotgunFunctionalizeR R-package 1.2-9 for Windows Download
- ShotgunFunctionalizeR R-package 1.2-9 for Mac OS X Download
Older versions of ShotgunFunctionalizeR can be found here
- ShotgunFunctionalizeR User's Guide (October 18, 2010) Download (PDF)
- ShotgunFunctionalizeR Reference Manual (October 26, 2010) Download
(PDF) [328 KiB]
- A ShotgunFunctionalizeR poster presented at FEMS 2009 Download (PDF) [2444
Requirements and Installation
ShotgunFunctionalizeR is dependent on the multtest package (Pollard at al., 2004
), which is a part of the Bioconductor software project. This means
that the Bioconductor needs to be installed on your computer before
ShotgunFunctionalizeR can function properly. To install Bioconductor,
start R and type:
After the installation of Bioconductor have finished, you can install
ShotgunFunctionalizeR by typing:
> install.packages("ShotgunFunctionalizeR", contriburl="http://shotgun.zool.gu.se")
If you use ShotgunFunctionalizeR in your research, please cite:
Kristiansson E, Hugenholtz P and Dalevi D. (2009). ShotgunFunctionalizeR: An
R-package for functional comparisons of metagenomes.
Contact Erik Kristiansson
(firstname.lastname@example.org) or Daniel Dalevi
(email@example.com) for more information.
Version 1.0 (last updated: 2010-10-26)